An external atmospheric pressure electrospray ionization source and electrostatic lenses for ion transport which was designed and constructed for an ion cyclotron resonance spectrometer has been improved by the addition of deflection plates. Picoampere ion currents have been trapped and accumulated with the result that high mass resolution for electrosprayed ions of 5-15,000 dalton molecular weight has been demonstrated. Deflection plates increase the effective duty cycle of the spectrometer, with a resulting important enhancement in signal intensity. Further improvements in the electrospray source and the ion cyclotron resonance spectrometer are anticipated, so that the resulting system can be used to measure the molecular weights of proteins and DNA fragments. Derivatization chemistry and separation conditions suitable for the detection of kynurenic acid and metabolites of cholorotryptophan analogs (indoleamine dioxygenase inhibitors) have been demonstrated using liquid chromatography-particle beam-negative chemical ionization mass spectrometry. Several derivatization reagents (substituted phenyl boronic acids) have been tested for use in forming cyclic boronates of glycols for improved detection in negative chemical ionization mass spectrometry. Organic ion imaging using tandem mass spectrometry has been refined so that spatially resolved mass selective images, representing a type of molecular or chemical microscopy can now be generated from non-conducting surfaces.